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GenotypeGVCFs reporting every site to have MQ0=0

dpoznikdpoznik StanfordMember

In the past, I’ve found MQ0 ("Total Mapping Quality Zero Reads") to be a very useful INFO feature of putatively variable sites. However, in my experience, GenotypeGVCFs reports every site to have MQ0=0, even those for which UnifiedGenotyper reports MQ0 > 0 when run on the same data. Is this a bug, or am I missing something?



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